Question

There are many types of molecular models, why are they referred to as a moving target in science?

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Answer 1

Molecules can be represented in many different ways such as (i) Stick Model (ii) Ball and Stick model (iii) Space-filling model

(i) Stick Model: This is elementary type most straightforward and easy representation of molecules by drawing of a line in which nuclei of bonded atoms are connected by lines.

(ii) Ball and Stick Model: This is a comparatively complicated method in which stick drawings are expanded with circles or balls of radii, in principle equal to a fraction number (e.g., 0.2) which corresponds to the van der Waals radii of atoms.

(iii) Space-filling model: The surface can also be represented either with dots or a solid surface. Such images are frequently called as space filling models. Often different atoms are shown in different colours in molecular images.

The balls represents different atoms in variety of colours: Black represents carbon (C); red, oxygen (O); blue, nitrogen (N); and white, hydrogen (H). Each ball is grounded with as many holes as its conventional valency (C: 4; N: 3; O: 2; H: 1) directed towards the vertices of a tetrahedron. Single bonds are represented by (fairly) rigid grey rods.

Molecular models are referred to as moving targets in science because during the docking process ligands search its position into the protein active site after a certain number of moves in its conformational space as the protein structure is not rigid in nature, usually it is a dynamic 3 dimensional structure. But the movement incorporates rigid body transformations such as translations and rotations, as well as internal changes to the ligand’s structure including torsion angle rotations. Hence molecular models are considered as moving targets in science.